[AMBER] Any help on how to implement it in cpptraj?

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Fri, 26 Apr 2019 16:25:11 +0000

I am trying to do ---->Analysis of MD simulations and clustering procedure.
I need to implement the leader algorithm for clustering according to the distance root mean square between two MD snapshots a and b,
which was calculated using the intermolecular distances dij between pairs of non-hydrogen atoms in acetonitrile and eight residues in the ABL-KINASE active site. A DRMS threshold of 1 ĒŠA is needed for clustering by the leader algorithm. The DRMS calculation does not require structural overlap."

Any input files how to implement it in cpptraj AMBER18?

I am trying to reproduce the methodology of " Small Molecule Binding to Proteins: Affinity and Binding/Unbinding Dynamics from Atomistic Simulations Danzhi Huang* and Amedeo Caflisch*"


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Received on Fri Apr 26 2019 - 09:30:02 PDT
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